/// <summary>
/// Add single Peptide-Spectrum match to RankTable.
/// </summary>
/// <param name="match"></param>
public void AddMatch(SpectrumMatch match)
{
var ranks = new RankedPeaks(match.Spectrum);
for (int i = 0; i < ranks.Peaks.Length; i++)
{
var index = i;
if (index >= MaxRanks)
{
index = MaxRanks - 1;
}
_rankTotals[index]++;
_rankTotals[MaxRanks]++;
}
foreach (var ionType in IonTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = ranks.RankIon(ion, _tolerance);
var rankIndex = GetRankIndex(rank);
_rankTable[ionType][rankIndex]++;
}
}
}
public void AddMatch(SpectrumMatch match)
{
foreach (var ionType in _ionTypes)
{
var charge = ionType.Charge;
var sequence = match.Sequence;
var pepSeq = ionType.IsPrefixIon
? sequence.GetRange(0, sequence.Count - 1)
: sequence.GetRange(1, sequence.Count - 1);
var ions = match.GetCleavageIons(ionType);
var nextIonIndex = 1;
while (nextIonIndex < ions.Count)
{
// look for peaks for current ion and next ion
_totalPairs++;
var currIonIndex = nextIonIndex - 1;
var currMz = ions[currIonIndex].GetMonoIsotopicMz();
var currPeak = match.Spectrum.FindPeak(currMz, _tolerance);
var nextMz = ions[nextIonIndex].GetMonoIsotopicMz();
var nextPeak = match.Spectrum.FindPeak(nextMz, _tolerance);
if (currPeak == null && nextPeak == null)
{
_ionPairFrequency[ionType].AddDatum(IonPairFound.Neither);
}
else if (nextPeak == null)
{
_ionPairFrequency[ionType].AddDatum(IonPairFound.First);
}
else if (currPeak == null)
{
_ionPairFrequency[ionType].AddDatum(IonPairFound.Second);
}
else
{
// found both peaks, compute mass error
_ionPairFrequency[ionType].AddDatum(IonPairFound.Both);
var aaIndex = (ionType.IsPrefixIon ? nextIonIndex : currIonIndex);
var aaMz = pepSeq[aaIndex].Mass / charge;
var massError = Math.Abs(nextPeak.Mz - currPeak.Mz) - aaMz;
_massError[ionType].AddDatum(massError);
}
nextIonIndex++;
}
}
}
public double GetScore(Sequence sequence, int charge, int scan, LcMsRun lcmsRun)
{
var mass = sequence.Composition.Mass + Composition.H2O.Mass;
var spectrum = lcmsRun.GetSpectrum(scan);
var ionTypes = _rankScore.GetIonTypes(charge, mass);
var filteredSpectrum = SpectrumFilter.FilterIonPeaks(sequence, spectrum, ionTypes, _tolerance);
var match = new SpectrumMatch(sequence, filteredSpectrum, charge);
var score = 0.0;
var rankedPeaks = new RankedPeaks(filteredSpectrum);
foreach (var ionType in ionTypes)
{
var ions = match.GetCleavageIons(ionType);
foreach (var ion in ions)
{
var rank = rankedPeaks.RankIon(ion, _tolerance);
score += _rankScore.GetScore(ionType, rank, charge, mass);
}
}
return(score);
}